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Volume 21 Supplement a December 2015 Next EMBnet.journal Volume 21 Supplement A December 2015 Next Generation Sequencing: a look into the future Final Conference & MC Meeting of COST Action BM1006 16-17 March 2015 Bratislava, Slovakia http://seqahead.eu/bratislava_2015 ESF provides COST is supported the Cost Office by the EU RTD through an EC Framework contract Programme EDITORIAL/CONTENT EMBnet.journal 21.A Editorial Contents The key task of COST Action BM1006, SeqAhead, Editorial ..............................................................2 Next Generation Sequencing (NGS) Data Analysis COST Action BM1006 (SeqAhead) closing Network, was, as its name suggests, networking; conference ........................................................3 but SeqAhead also emphasised the dissemina- Scientific Programme.........................................5 tion of knowledge. During the four years of the Keynote Lectures ................................................9 Action, SeqAhead surpassed every expectation: Oral Presentations ........................................... 13 with members participating from 29 European Posters.......................................................................25 countries, plus one international partner from South Africa, the Management Committee mem- bership reads like a “who’s-who” of European NGS research. This EMBnet.journal Conference Supplement clearly shows that during the four years of SeqAhead’s existence, the Action members ac- tively shared software and experiences, and col- laborated in numerous projects spanning diverse EMBnet.journal Executive Editorial topics – from those at the biological end of the spectrum to those at the informatics end. Board SeqAhead was acknowledged in more than Erik Bongcam-Rudloff, Department of Animal Breeding and Genetics, SLU, SE 100 peer-reviewed articles, demonstrating that [email protected] the Action’s activities benefited a large and wide audience. Teresa K. Attwood, Faculty of Life Sciences and School of Computer Science, University of Manchester, UK [email protected] EMBnet.journal Editorial Board Domenica D’Elia, Institute for Biomedical Technologies, CNR, Bari, IT [email protected] Andreas Gisel, Institute for Biomedical Technologies, CNR, Bari, IT [email protected] Laurent Falquet, University of Fribourg, Fribourg, CH [email protected] Pedro Fernandes, Instituto Gulbenkian. PT [email protected] Lubos Klucar, Institute of Molecular Biology, SAS Bratislava, SK [email protected] Vicky Schneider-Gricar, The Genome Analysis Centre (TGAC) Norwich, UK [email protected] Cover picture: Valparaiso, Chile, 2015 [© Erik Bongcam-Rudloff] page 2 (not for indexing) EMBnet.journal 21.A REPORTS e860 COST Action BM1006 (SeqAhead) During the conference, keynote and selected speakers presented the latest NGS technologies closing conference “Next Generation and their applications, discussed storage and Sequencing: a look into the future” analysis systems, and presented the training available and still required to enable researchers to utilise these technologies in new fields of re- search. The event opened with a short welcome from the local organiser, Dr. Lubos Klucar (IMB SAS, Bratislava (SK)), followed by an introduction by the SeqAhead Chair, Prof. Erik Bongcam-Rudloff (SLU, Uppsala (SE)). Fourteen speakers presented their work and discussed new technology highlights in the field, including the latest minION device Lubos Klucar 1, Teresa K. Attwood 2, Erik presented by Ola Wallerman (SLU, Uppsala (SE)). Bongcam-Rudloff 3 The final SeqAhead MC meeting took place 1Institute of Molecular Biology, Slovak Academy of Sciences, during the second day, where the principal Bratislava, Slovakia achievements from the four years of the Action 2 University of Manchester, Manchester, United Kingdom were presented and discussed. The impact of 3Swedish University of Agricultural Sciences, Uppsala, Sweden the project has been multi-faceted, ranging Klucar L et al. (2015) EMBnet.journal 21(Suppl A), e860. http:// from the very abstract ‘improved healthcare’, dx.doi.org/10.14806/ej.21.A.860 owing to better trained NGS researchers in medi- cal diagnostic facilities, to the very concrete, in The closing conference and final Management terms of the research described in the nearly 100 Committee (MC) meeting of COST Action peer-reviewed journal articles that acknowledge BM1006 (SeqAhead) took place over two days, SeqAhead. 16-17 March 2015, in Bratislava (SK). Fifty par- Doubtless, the most tangible result of ticipants from 20 European countries gathered SeqAhead is the large number of students/scien- at the event to discuss and share experiences, tists who gained access to high-quality training in know-how related to new technologies, and key the emerging field of NGS, training that is not yet developments in the field of Next Generation part of most formal university curricula, and was Sequencing (NGS) research. SeqAhead COST conference participants. page 3 (not for indexing) e860 EMBnet.journal 21.A REPORTS certainly not available to scientists who complet- ed their studies a few years ago. SeqAhead organised more than 30 work- shops, four conferences with more than 150 par- ticipants each, and several schools, each with 25-60 students. In total, almost 2,000 scientists participated in these activities, the impact of which has been immediate for NGS research in Europe, and will continue to be felt for many years. As already mentioned, SeqAhead partners have published about 100 articles on NGS and Poster session. related topics, and many more publications are expected beyond the end of the project. Such articles help disseminate the scientific activities entific interests in formal and informal settings, catalysed by SeqAhead and, we hope, will have and in physical and virtual (video) meetings. a lasting impact: healthcare is a major financial These meetings led to the formation of several burden in most European countries, so better large European collaborations, such as the (now 1 NGS science in hospitals is likely to have both so- complete) AllBio project and the newly awarded 2 cietal and economic benefits. COST Action CHARME , which is to kick-off in 2016. SeqAhead brought together researchers from AllBio, in turn, triggered the establishment of the 3 across Europe, allowing them to discuss their sci- recently initiated EU project PROLIFIC . Members of SeqAhead also won an IRSES Marie Curie pro- ject aiming to create an NGS network between the Americas and Europe4. We expect these new projects to have a lasting impact in many areas of life-science re- search, we are proud to have been part of the successful network that seeded them, and we wish them success in the years ahead. Finally, our thanks go out to all who made SeqAhead such a warmly collaborative and productive pro- ject! Lubos Klucar (Local Organiser), Teresa K. Attwood (Action Vice Chair) and Erik Bongcam- Jim Dowling (KTH - Royal Institute of Technology) having talk Rudloff (Action Chair) on the biobankcloud project (www.biobankcloud.com). 1 www.allbioinformatics.eu/doku.php 2 www.cost.eu/COST _ Actions/ca/CA15110 3 euprolific.eu/index.php/the-project 4 www.deann.eu page 4 (not for indexing) Scientific Programme COST Action BM1006 - Final Conference 16-17 March 2015, Bratislava, Slovakia EMBnet.journal 21.A Scientific Programme 16 March COST Conference “NGS: a look into the future” 08:30-09:00 Registration and Coffee 09:00-09:20 Welcome from organisers NGS Technologies and their Applications 09:20-10:00 Keynote Lecture Session Chair: Erik Bongcam-Rudloff Power and Limitations of RNA-Seq: Findings from the SEQC (MAQC-III) consortium Paweł Łabaj Chair of Bioinformatics Research Group, Boku University Vienna, Austria 10:00-10:30 Coffee Break & postesr set-up 10:30-12:00 Oral Presentations Reproducible Research in the era of Next Generation Sequencing: current approaches, examples and future perspectives Claudia Angelini, Dario Righelli, Francesco Russo Current status of nanopore sequencing using the minION device – from full length cDNA sequencing to genome assembly improvements Ola Wallerman Deep insights into Mecp2-driven transcriptional (de)regulation at embryonic developmental stage through RNA-Seq data analysis Kumar Parijat Tripathi, Maurizio D'Esposito, Mario R Guarracino, Marcella Vacca Exploring the activity of microorganisms in the forest soil using metatranscriptomics Petr Baldrian 12:00-13:00 Lunch Storage and Analysis Systems 13:00-13:40 Keynote Lecture Session Chair: Ralf Herwig Population-Scale Genomics with BiobankCloud and Hops/Hadoop Jim Dowling KTH - Royal Institute of Technology, Stockholm, Sweden 13:40- 15:00 Oral Presentations Creating a successful facility for large-scale extraction of DNA, an example from the Swedish biobank initiative BBMRI.se James Thompson Using neural networks to filter predicted errors in NGS Data Dimitar Vassilev, Milko Krachunov DIANA-TarBase v7: indexing thousands experimentally supported miRNA:mRNA interactions Dimitra Karagkouni Biobanking for the future, how to prepare for the next generation of next generation sequencing Tomas Klingström 15:00-15:30 Coffee Break 15:30-16:10 Keynote Lecture Session Chair: Claudia Angelini Data deluge demands training tsunami Eija Korpelainen CSC, Espo, Finland 16:10-17:10 Oral Presentations Introducing Meta2genomics: the search for the “micro-bee” Jose R Valverde page 6 (not for indexing) 21.A EMBnet.journal 16:10-17:10 Oral Presentations Introducing Meta2genomics: the search for the “micro-bee” Jose R Valverde
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